Added RMSD code re issue #50
Better input tests in wrapper
Merge remote-tracking branch 'upstream/master' into rmsd
Swapped traj1 and traj1
Merge remote-tracking branch 'upstream/master' into rmsd
added some simple performance testing
aded a post to appspot
added performance tests for each of the readers and writers
add performance plots generated in IPython notebook / R
some pep8 fixes
some pep8 fixes
more flake8 fixes
performance plots dont belong here
don't want nonzero exit status from flake8
added test (that fails) showing multiframe pdb doesn't work
Fixes for robert
THis adds multiframe support to the pdb reader
added another test ot the pdb parser
add a test to ensure that if there's a mismatch between the number of atoms in the xtc and the number of atoms in the topolgy, i.e. msmbuilder issue #188, that we throw an informative error message
Possibly working alignment.py